Re: [chimera-dev] Strange behavior, crashing, etc.
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Hi Geoff, Eric Pettersen tells me Chimera is hanging when you display diamond.pdb in ball and stick or sphere mode because it is searching for rings. There are too many rings to find. Eric will look at fixing the ring finding code. The reason it needs to know the rings for some display modes is so it can identify atom types (classed by connectivity) so it can assign correct atom radii. You can work around the problem by issuing a Chimera command to set the vdw radii before using ball and stick or sphere display. Use Favorites/Command Line and type a command like vdwdefine * * 1.0 This example sets all atom radii to 1 angstrom (for sphere display). See the User's Guide under Commands for details on setting the radii of specific atoms if you want different atoms shown with different sizes. Any application, Aqua or not, can have an icon in the Dock -- it just has to be packaged with the Mac App directory layout and have an icon file. But Force Quit apparently only lists Aqua applications. The Aqua version of Chimera is shown in the Force Quit list. Tom
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chimera-users@cgl.ucsf.edu